IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

2020/01/22 by Bui Quang Minh, Bùi Quang Minh, Heiko A Schmidt +7 · 842 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Evolution and Paleontology Studies #Genetic diversity and population structure #Genomics and Phylogenetic Studies

paper · pdf · doi:10.1093/molbev/msaa015

openalex publication_date 2020/01/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

Abstract

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

Citations

• Ultrafast Approximation for Phylogenetic Bootstrap
• Evolutionary trees from DNA sequences: A maximum likelihood approach
• Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial
• IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
• Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

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• Integrative Taxonomy Reveals the First Record of <i>Diaporthe manihotia</i> in Russia and Resolves the Status of <i>Diaporthe betae</i> Within the <i>D. manihotia</i> Species Complex
• Evidence for Cryptic Sex in <i>Escovopsis</i> , a Mycoparasite in the Fungus-Growing Ant Symbiosis
• Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga <i>Auxenochlorella</i>
• A deeper look into the diversity of Phyllium leaf insects from Indonesia: seven new species and two unique egg morphologies (Phasmatodea, Phylliidae)
• Studies in Lepiota (Agaricales, Verrucosporaceae): supporting the merger of Chamaemyces into Lepiota and proposing two new species
• Phylogenomic blind spots: the limits of UCE and BUSCO loci in the presence of gene flow
• Diversification in ANME-1 archaea is associated with the presence of highly variable genomic hotspots
• Evolution of genome size and GC content in the tribe Carduinae (Asteraceae)
• Evolutionary conservation and divergence of phagocytic and coagulation programs across bilaterian circulating immune cells
• Gelada genomes highlight events of gene flow, hybridisation and local adaptation that track past climatic changes
• An episodic burst of massive genomic rearrangements and the origin of non-marine annelids
• AliFilter: a machine learning approach to alignment filtering
• Updated taxonomy of the family Rhizobiaceae with proposals for 8 novel genera and 32 novel combinations
• Rediscovery and phylogenomic placement of <i>Feliciadamia stenocarpa</i> (Feliciadamieae: Melastomataceae): assessing gene tree discordance
• The Sensory Shark: High-quality Morphological, Genomic and Transcriptomic Data for the Small-spotted Catshark <i>Scyliorhinus Canicula</i> Reveal the Molecular Bases of Sensory Organ Evolution in Jawed Vertebrates
• The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes
• Reliable Inference of Phylogenomic Relationship via Assembly‐Based Strategy Accommodating Raw Reads and Proteins
• Expansion and loss of sperm nuclear basic protein genes in Drosophila correspond with genetic conflicts between sex chromosomes
• Integrative taxonomy of a new giant deep-sea caudofoveate from South China Sea cold seeps
• BUSCO: Assessing Genomic Data Quality and Beyond
• Structural Basis of Lipopolysaccharide Assembly by the Outer Membrane Translocon Holo-Complex
• Repeated loss of function at HD mating-type genes and of recombination in anther-smut fungi
• Bringing Shadowdragons to light: Neurocordulia (Anisoptera: Corduliidae) systematics
• A Streptomyces megacluster encodes synergistic biotin-targeting antibiotics
• Protist-dominated hard substrate faunas thrive at the deepest ocean depths
• Continuous colonization of the Atlantic coastal rain forests of South America from Amazônia
• Maximising informativeness for target capture-based phylogenomics in Erica (Ericaceae)
• Repeated duplications and losses shaped SMC complex evolution from archaeal ancestors to modern eukaryotes
• AOC: Analysis of Orthologous Collections -- an application for the characterization of natural selection in protein-coding sequences
• CoExpPhylo – A Novel Pipeline for Biosynthesis Gene Discovery
• Host adaptation is driving genome evolution and ecological speciation in the ectomycorrhizal basidiomycete <i>Tricholoma</i>
• Refining generic limits in Hyacinthinae (Asparagaceae, Scilloideae): Conflict and concordance between morphology and phylogenomics
• Predictors of Protein Evolution in the drosophilid Immune System
• Modelling compositional and exchange rate changes over time
• A hot origin of dissimilatory sulfite reduction catalyzed by DsrAB in the Paleoarchean Era
• Structure and mechanism of antiphage retron Eco2
• Harnessing Bulk‐Segregant Mapping to Identify Trait‐Associated Genes in the Allopolyploid Model Plant <i>Nicotiana benthamiana</i>
• Taxonomic and phylogenetic insights into dipteran-parasitizing Ophiocordyceps: Descriptions of two new species and a new record from China and Laos
• Genomics of Sable ( <i>Martes zibellina)</i> × Pine Marten ( <i>Martes martes</i> ) Hybridization
• Structural and evolutionary insights into the isoprene monooxygenases
• Resolving the taxonomic enigma of Nesocaryum stylosum (Boraginaceae): phylogenetic evidence for its reclassification as Cryptantha stylosa
• Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin
• Global dispersal and diversification in ground beetles of the subfamily Carabinae
• Distribution of a novel DsrEFH sulfur transferase suggests widespread sulfur oxidation capacity in sulfate reducers
• Urea use drives niche separation between dominant marine ammonia oxidizing archaea
• Near‐complete genome assembly of a transformation‐efficient elite inbred line LH244 and its comparison with B73
• Genomic Insights into Historical Adaptation of Three Key Fungal Plant Pathogens
• Two new species of genus Leucoagaricus and Leucocoprinus (Agaricaceae, Agaricales) from China
• Phylogenomics and genetic admixture of the invasive fireweed complex (Senecio inaequidens–Senecio madagascariensis) at a global scale
• Genomic evidence for the phylogeny, evolution, and classification of <i>Orostachys</i> s.l. (Crassulaceae): One, two, or three genera?
• Mitonuclear Discordance of Beetles Shaped by Incomplete Lineage Sorting and Introgression Under Loose Interaction Mechanism
• Molecular and Functional Divergence of Zebrafish Sox Paralogs Controlling Endoderm Formation and Left–Right Patterning
• Integrating Sanger and next‐generation sequencing data sheds light on phylogenetic relationships among gelechioid moths (Lepidoptera: Gelechioidea)
• RECUR: identifying recurrent amino acid substitutions from multiple sequence alignments
• Pre-existing neutralizing antibodies against cattle-transmitted influenza A virus H5N1 are detectable in unexposed individuals
• Genetic diversity and evolutionary dynamics of Senecavirus A in Brazil
• Ancestral Sequence Reconstruction Provides Insights into the Structural Diversification and Neofunctionalization of T-superfamily Conotoxins in <i>Conus</i>
• Genome Variation in Three <i>Anthophora</i> Bee Species Reflects Divergent Demographic Histories
• Healthcare Infrastructure Shapes Evolutionary Trade-offs and Geographic Dissemination of Multidrug-Resistant <i>Acinetobacter baumannii</i>
• Genomic and Phenotypic Delimitation of Species in a Temperate Aquatic Biodiversity Hotspot
• Environmental Variation Promotes Convergent Evolution and Rapid Diversification of Wing Shape and Color in Skipper Butterflies
• Mitochondrial Gene Phylogenetic Incongruencies Are Linked to Chromosomal Position and Function
• Evolution of the Tri-PDZ Domain in PSD95 (DLG-4 Gene)
• Neo-sex Chromosomes Track the Mitochondrial Phylogeny and Exhibit an Extensive Added Stratum of Recombination Suppression in Honeyeaters (Aves: Meliphagidae)
• Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants
• Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning
• Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions
• Thermostable Bacterial Esterases From Lipase Family 1.5 Degrade Compostable Polyesters PBAT and PBSA
• High‐Quality Genome Assembly of <i>Diplocarpon coronariae</i> Unveils <scp>LTR</scp> Retrotransposon‐Driven Structural Dynamics in Fungi Evolution
• Genomic investigations in animal enteric disease-associated Clostridium perfringens
• Unveiling an asymmetric plant–fungal symbiosis: morphological, cytogenetic, and molecular characterization of a haploid Epichloë festucae strain associated with three polyploid cytotypes of the Iberian endemic grass Festuca rothmaleri
• Assessing phylogenetic confidence at pandemic scales
• The Endosymbiont Consortia of Two Cixiidae Planthoppers Reveal an Ancient Symbiosis With ‘ <i>Candidatus</i> Mirabilia Symbiotica’
• The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals
• A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
• Are interphylum spiralian relationships resolvable?
• A new entoproct commensal on holothuroids in the northwestern Pacific abyssal–hadal zone
• Structural basis of the catalytic and allosteric mechanism of bacterial acetyltransferase PatZ
• Pseudogenization of the chaperonin system in ‘Candidatus Phytoplasma pruni’ revealed by genome sequencing and comparative genomics
• A simple cell-cycle control system in <i>Marchantia polymorpha</i> provides a framework for understanding plant cell proliferation
• Redox gradients define the ecological niche of ciliates with denitrifying endosymbionts in anoxic lake waters
• Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta
• Homologs of yeast polyamine uptake transporters are dispensable for polyamine uptake but affect adaptation to inorganic nutrients, conidiation, and DON production in <i>Fusarium graminearum</i>
• Revised Evolutionary and Taxonomic Synthesis for Parrots (Order: Psittaciformes) Guided by Phylogenomic Analysis
• Chromosome‐level genome assembly and resequencing reveal the genomic basis of two ornamental traits in White Cloud Mountain minnow ( <i>Tanichthys albonubes</i> )
• Molecular evolution of the Wood-Ljungdahl pathway and the reductive glycine pathway in Desulfobacterota
• Review of the subgenus Paropheltes Cameron of genus Netelia Gray (Hymenoptera, Ichneumonidae, Tryphoninae) from Taiwan, with a proposal for improving male genitalia observations
• <i>Decodon erythroleukos</i> , a new deepwater species of hypsigenyin wrasse ( <scp>Teleostei: Labridae</scp> ) from the western <scp>Pacific Ocean</scp>
• From North to South: transmission dynamics of H1N1pdm09 swine influenza A viruses in Italy
• Dairy cows inoculated with highly pathogenic avian influenza virus H5N1
• Whole-genome-based phylogenetic analyses provide new insights into the evolution of springtails (Hexapoda: Collembola)
• Investigation and control of an outbreak of methicillin-susceptible <i>Staphylococcus aureus</i> skin and soft tissue infections in a neonatal intensive care unit.
• Evolutionary and structural bioinformatics identifies GPR89 as a conserved member of the LIMR protein superfamily
• Onygenales from marine sediments: diversity, novel taxa, global distribution, and adaptability to the marine environment
• Moving Beyond Morphology: Genomic Insights Into Evolutionary Histories of Haplosclerid Sponges
• A Deeply Branching Lineage in Heterolobosea (Discoba) With Multiflagellated and Multigrooved Life Stages
• Neillia daloushanensis, a new species of Neillia (Rosaceae) from southwest China
• Phylogenetic Analysis of <i>Scaphoideus</i> Reveals New Insights Into the Invasion History of <i>Scaphoideus titanus</i> (Hemiptera, Cicadellidae) in Europe
• Apiaceae FNS I originated from F3H through tandem gene duplication
• Opposing roles of pseudokinases NRBP1 and NRBP2 in regulating L1 retrotransposition
• Isolation and genetic characterization of a novel Kevo orbivirus and a strain of Mobuck virus from Ochlerotatus communis mosquitoes in Finland
• Spatiotemporal prevalence and characterization of the lineage I insect-specific flavivirus, Quang Binh virus, isolated from Culex gelidus mosquitoes in Singapore
• New fossil species of Trechinae (Coleoptera: Carabidae) from mid-Cretaceous French amber helps refining the age of the subfamily and its tribes under total-evidence dating
• Genomics reveals zoonotic and sustained human mpox spread in West Africa
• The virulence regulator CovR boosts CRISPR-Cas9 immunity in Group B Streptococcus
• Are reads required? High-precision variant calling from bacterial genome assemblies
• The highly diverse repertoire of transposable elements within the genomes of parasitic wasps (Hymenoptera: Braconidae)
• Evolutionary Insights into the Length Variation of DNA Damage Response Proteins Across Eukaryotes
• Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library
• An integrative approach to alpha taxonomy in Erica L. (Ericaceae) with three new species from the Western Cape, South Africa
• Genomic patterns in the dwarf kingfishers of northern Melanesia reveal a mechanistic framework explaining the paradox of the great speciators
• Phylogenomic analysis reveals the evolutionary history of Paleartic needle-leaved junipers
• 2-Oxoglutarate-dependent dioxygenases contribute to cardenolide biosynthesis in <i>Erysimum cheiranthoides</i> (wormseed wallflower)
• Three new species of &lt;i&gt;Alpova&lt;/i&gt; from Japan: new insights into biogeography in &lt;i&gt;Alpova&lt;/i&gt;
• Rapid divergence with gene flow creates intractable nodes in the tree of life: an empirical demonstration in the buzzing flowerpecker ( <i>Dicaeum hypoleucum</i> )
• Genome-wide phylogeny reshapes our understanding of the evolution of deep-sea dragonfishes, bristlemouths, viperfishes, and allies (Stomiiformes)
• New Methods to Calculate Concordance Factors for Phylogenomic Datasets
• Enamel proteins reveal biological sex and genetic variability within southern African <i>Paranthropus</i>
• Population genomic analysis unravels the evolutionary processes leading to budding speciation
• Six Newly Sequenced Chloroplast Genomes From Quadriflagellate Chlamydomonadales (Chlorophyceae): Phylogeny and Comparative Genome Analyses
• Reconstruction of Ancestral Protein Sequences Using Autoregressive Generative Models
• Metagenomic mining reveals novel viral histones in dsDNA viruses
• Optimization and Evaluation of the <scp>bestRAD</scp> Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, <i>Bactrocera dorsalis</i>
• Genome and Tissue‐Specific Transcriptome of the Tropical Milkweed ( <scp> <i>Asclepias curassavica</i> </scp> )
• Prolonged persistence of mutagenic DNA lesions in somatic cells
• Molecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory
• A new species and a new genus of the family Axinidae (Polyopisthocotyla: Mazocraeidea) parasitic on Japanese halfbeak Hyporhamphus sajori (Beloniformes: Hemiramphidae) collected from the Seto Inland Sea, Japan
• Towards a unifying phylogenomic framework for tailed phages
• A phylogenetically informed generic reclassification of the hemionitid ferns (Pteridaceae: Cheilanthoideae)
• Genome skimming for improved phylogenetics of Taiwanese phasmids (Insecta: Phasmatodea)
• High‐Throughput Evaluation of Natural Diversity of F‐Type <scp>ATP</scp> Synthase Rotor Ring Stoichiometries
• Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains
• Phylogenetic position and description of two new species of the land planarian genus Amaga (Platyhelminthes: Tricladida: Geoplaninae) and synonymization of Bogga
• The chromosome-level genome assembly of an endangered herb<i>Bergenia scopulosa</i>provides insights into local adaptation and genomic vulnerability under climate change
• Novel gene arrangement in the mitochondrial genome of <i>Aspersentis megarhynchus</i> (Acanthocephala, Echinorhynchida, Heteracanthocephalidae), and its phylogenetic implications
• Evolutionary History and Ecology of <i>Andrena</i> ( <i>Foveoandrena</i> ) <i>androfovea</i> : A New Nearctic Mining Bee (Hymenoptera, Andrenidae) Species and Subgenus
• Comparative pangenome analysis of major pneumococcal genotypes from India
• Thirty novel fungal lineages: formal description based on environmental samples and DNA
• Rational design of induced regeneration via somatic embryogenesis in the absence of exogenous phytohormones
• Phylogenomic approach to integrative taxonomy resolves a century‐old taxonomic puzzle and the evolutionary history of the <i>Acromyrmex octospinosus</i> species complex
• Likelihood-free inference of phylogenetic tree posterior distributions
• Comparative genomics of the highly halophilic Haloferacaceae
• Genomic surveillance reveals a dengue 2 virus epidemic lineage with a marked decrease in sensitivity to Mosnodenvir
• Fur microbiome as a putative source of symbiotic bacteria in sucking lice
• Description of a new genus and species of Euptychiina (Lepidoptera: Nymphalidae) from the Brazilian Amazon rainforest
• Bacteria in honeybee crops are decoupled from those in floral nectar and bee mouths
• Horizontal transfers of polydnavirus segments extend the known range of parasitoid attacks to stick insects and orthopterans
• Global distribution of isoprenoid quinones across Bacteria
• A <i>k-</i>mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data
• Complex genomes of early nucleocytoviruses revealed by ancient origins of viral aminoacyl-tRNA synthetases
• No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2
• Acinetobacter pengchengensis sp. nov., isolated from the urban wastewater of Shenzhen, Guangdong Province, China
• Evolutionary History of the <i>α-Carbonic Anhydrase</i> Gene Family in the Phylum Arthropoda, With Comparisons to <i>αCA</i> in Chordates
• Fusobacterium abscessus sp. nov., associated with brain abscess in humans
• From soil to sea: unravelling the metabolic versatility and social dynamics of Myxococcota bacteria from different Danish environments
• Biased Estimates of Phylogenetic Branch Lengths Resulting from the Discretised Gamma Model of Site Rate Heterogeneity
• Comprehensive profiling of insertion sequences and eukaryotic-like transposons across archaeal genomes
• Comparative genomic and network analysis of Methanocaldococcus genus reveals genetic diversity and adaptive metabolic traits
• A Lepidoptera Synthesis Phylogeny of 11,001 Species and Its Application in Phylogenetic Profiling of Herbivore DNA Barcodes: Towards an Integrative Phylogenetic Framework for Insects
• Unravelling a Rapid Radiation: Biogeography and Niche Evolution of <scp> <i>Carex</i> sect. <i>Echinochlaenae</i> Kük </scp> . (Cyperaceae)
• Stony secrets unveiled: evolution of hypercalcified calcareous sponges (Porifera)
• The Effects of Hemiplasy and Maintained Polymorphisms in Fossil Clades
• Phylogeny-aware comparative genomics of Vibrio vulnificus links genetic traits to pathogenicity
• Tepsin and AP4 mediate transport from the trans-Golgi to the plant-like vacuole in toxoplasma
• Phylogenomics and intergenomic conflict in a challenging orchid clade (Calypsoinae): monophyly of <i>Corallorhiza</i> , paraphyly of <i>Oreorchis</i> , and resurrection of <i>Kitigorchis</i>
• The oldest Gondwanan non-biting midge (Diptera, Chironomidae, Podonominae) sheds light on the historical biogeography of the clade
• Linking fluvial barriers and habitat specialization in the evolution of microendemism in riverine fishes
• Reconstructing ancient dispersal through Antarctica: A case study of stream‐inhabiting beetles
• Convergent Evolution in Amblyopsid Cavefishes and the Age of Eastern North American Subterranean Ecosystems
• The gold-ringed octopus (Amphioctopus fangsiao) genome and cerebral single-nucleus transcriptomes provide insights into the evolution of karyotype and neural novelties
• Ancient climate changes and relaxed selection shape cave colonization in North American cavefishes
• Desulforhopalus glucosivorans sp. nov., a sulphate-reducing bacterium isolated from brackish lake sediment
• Unveiling coralline diversity of mesophotic rhodoliths in subtropical Japan, including new species of <i>Sporolithon</i> , emended genera <i>Orientalilithon</i> and <i>Roseolithon</i> (Corallinophycidae, Rhodophyta)
• Cultural transmission and genomic co-divergence in the willow tit across the Palearctic
• New additions to Omphalotaceae (Agaricales, Basidiomycota): two new rhizomorph-forming species from China
• Population Genomics of <i>Pseudocercospora griseola</i> Reveals New Groups in the Middle American Clade and the Presence of the Endophytic Bacterium <i>Achromobacter xylosoxidans</i>
• Phreatobacter aquiterrae sp. nov., isolated from an Icelandic subsurface geothermal aquifer
• Multiple origins and functions: evolutionary pathways of HSP70 proteins in viruses
• Identification of two <i>Wolbachia</i> genes with cell proliferation-inhibitory activity in <i>Ostrinia</i> cultured cells
• Lateral gene transfer introduced the microbial anaerobiosis-related gene <i>rquA</i> into early animals
• Zinc Transporters in Diseases, Including Diabetes and Related Conditions
• CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation
• Unravelling the genomic landscape of Canadian Borrelia burgdorferi: a comparison across global strains
• Ameles spallanzania (Insecta, Dictyoptera): A newly introduced species of Mantodea in Crimean fauna
• Molecular bases of circadian magnesium rhythms across eukaryotes
• Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility
• Cattle manure suppresses methane consumption and enhances denitrification-associated nitrous oxide production in farm dams
• Integrative taxonomy of Madagascar’s sand-swimming skinks (Scincidae: <i>Voeltzkowia</i> , <i>Grandidierina</i> ) and preliminary evidence for an overlooked inland belt of white sand patches across the island’s west
• Revision of Amana yunjuensis (Liliaceae) based on morphological and molecular evidence: synonym of Amana anhuiensis
• Phylogenomics and biogeography of the cleptoparasitic bee genus <i>Triepeolus</i> Robertson (Hymenoptera: Apidae), with a revised subgeneric classification of <i>Triepeolus</i> and its sister genus, <i>Epeolus</i> Latreille
• Genomic architecture and evolution of heterostyly: new insights from <i>Cordia subcordata</i> (Boraginaceae)
• Discovery and Evolutionary Analysis of a Novel Genus of Endogenous Pararetroviruses with Long Terminal Repeats
• RETRACTED: Integrative phylogenomics positions sponges at the root of the animal tree
• Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order
• Unveiling the tempo of molecular and morphological evolution across the Tree of Life
• Diversification of the Staphylococcal Cassette Chromosome Through Distinct Mechanisms of Horizontal Transfer
• Robust phylodynamic inference and model specification for HIV transmission dynamics
• PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
• Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium
• Evolution of Sex-Biased Gene Expression During Transitions to Separate Sexes in the <i>Silene</i> Genus
• <i>Magniporophytum</i> gen. nov. and <i>Orientalilithon</i> gen. nov. (Hapalidiales, Corallinophycidae): Two new genera of coralline red algae from the Pacific Ocean, including the description of three new species
• Bacterial warfare is associated with virulence and antimicrobial resistance
• Phylogenomic timetree-calibrated speciation clocks for Caenorhabditis nematodes reveal slow but disproportionate accumulation of post-zygotic reproductive isolation
• A new large violin spider from Argentina, with a discussion on the homology and evolution of female genital structures in Loxosceles (Araneae: Sicariidae)
• Comparative genomics of sex determination related genes reveals shared evolutionary patterns between bivalves and mammals, but not <i>Drosophila</i>
• A fungal <scp>sRNA</scp> silences a host plant transcription factor to promote arbuscular mycorrhizal symbiosis
• Importance of De Novo Gene Evolution to Emerging Viral Threats: The ORF10 Strain-Restricted Orphan Gene of SARS-CoV-2 Promotes Pathogenesis
• Phylogenetics and evolution of <i>Digitaria</i> grasses, including cereal crops fonio, raishan and Polish millet
• Big jaw, small genome: first description of the mitochondrial genome of <i>Odontomachus</i> (Formicidae, Ponerinae): evolutionary implications for Ponerinae ants.
• Phylogeography and karyotypic evolution of some Deuterodon species from southeastern Brazil (Characiformes, Characidae, Stethaprioninae)
• Arthropod <i>Pax</i> Gene Evolution: A Role for <i>Vanessa Cardui Twin of Eyeless</i> in Eye Development
• Distinct Evolutionary Signatures of Human Parainfluenza Viruses 2 and 4 Reveal Host Antagonism Divergence and Phylogenetic Discordance
• Diversity of Niphargus (Crustacea, Amphipoda) in France, as revealed by DNA barcoding approach
• Ecosystem retrogression enhances cross‐domain microbial stability and increases the genetic potential for nutrient cycling
• Phylogenetic position and mitochondrial genome evolution of “orphan” eukaryotic lineages
• Discovery of a novel Keithomyces species isolated from the sclerotia and a new Papiliomyces from Southwest China: Integrated taxonomy based on morphology and phylogeny
• Genomic Prediction of Disease Resistance Provides a Path to Marker Assisted Restoration in a Wetland Foundation Tree Species
• A new large predator (Amphipoda, Eusiridae) hidden at hadal depths of the Atacama Trench
• The phylogenetic affinities of Chaetognathifera, with considerations of systematic error and the robusticity of macrosyntenic results
• Mitogenomic sequencing of the Brazilian Mastiff and Brazilian Terrier suggests a complex scenario of breed formation for two established Brazilian dog breeds
• A notable geographic and environmental extension of <i>Lutreolina massoia</i> (Didelphimorphia: Didelphidae): first record for Peru
• Phylogenomics resolves the evolutionary histories and taxonomy of the long‐associated North American legume genera <i>Psorodendron</i> and <i>Psorothamnus</i>
• Assembly, Characterization and Comparative Analysis of the Complete Mitogenome of Small-Leaved Eriobotrya seguinii (Maleae, Rosaceae)
• Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges
• Phylogenetic Insights and a New Distribution Map for Chile's Endemic <i>Virilastacus</i> Crayfishes
• Mustura arenaria, a new species of genus Mustura (Cypriniformes, Nemacheilidae) from Myanmar, with taxonomic notes on Mustura shanensis
• Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus <i>Ophrys</i> )
• The visual system of the longest-living vertebrate, the Greenland shark
• Climate niches structure a regional hybrid zone in <i>Sphagnum</i> (peatmoss, Bryophyta)
• Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks
• Morphological and phylogenetic analysis of the early-diverging lineage of Glomeromycota suggest two new genera and recombinations in Archaeosporales
• The hidden life of <i>Xylella</i> : mining the NCBI Sequence Read Archive reveals potential new species, host plants, and infected areas for this elusive bacterial plant pathogen
• Untangling the colonization history of the Australo-Pacific reed warblers, one of the world’s great island radiations
• Origin and evolution of West Nile virus lineage 1 in Italy
• A virus associated with the zoonotic pathogen <i>Plasmodium knowlesi</i> causing human malaria is a member of a diverse and unclassified viral taxon
• Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail
• A phylogenetic contribution to understanding the panzootic spread of African swine fever: from the global to the local scale
• The Evolutionary History and Modern Diversity of Triterpenoid Cyclases
• Population immunity predicts evolutionary trajectories of SARS-CoV-2
• Inverse Latitudinal Diversity Gradient, Systematics and Historical Biogeography in the Gomphocerinae Grasshoppers (Orthoptera, Acrididae)
• Sinosenecio yaanensis (Asteraceae, Senecioneae), a new species from western Sichuan, China
• Reinstatement of Hellwigia Warb. (Zingiberaceae) and its molecular and morphological delimitation
• Bioprospecting of Chilean Labyrinthulomycetes: Laboratory Evaluation of <scp>PUFA</scp> and Carotenoid Production in Isolates From Diverse Natural Environments
• Hidden Markov Model-Based Prokaryotic Genome Space Mining Reveals the Widespread Pervasiveness of Complex I and Its Potential Evolutionary Scheme
• Unraveling nitrogen uptake and metabolism: gene families, expression dynamics and functional insights in aspen ( <i>Populus tremula</i> )
• There is gold in the graveyard: a new lineage of zombie-ant fungi in the genus <i>Ophiocordyceps</i> ( <i>Ophiocordycipitaceae</i> : <i>Hypocreales</i> ) from Minas Gerais, Brazil
• Gondwanan Origin of Bark and Ambrosia Beetles and Their Rapid Worldwide Diversification During the Cretaceous
• Population genomics of rainforest mountain frogs (Anura: Limnodynastidae: Philoria) severely impacted by the Australian megafires
• A new species, Didymoglossum radiatum (Hymenophyllaceae), and two new records with note to the genus Didymoglossum Desv. from Thailand
• Progress towards a monophyletic <i>Ozothamnus</i> (Asteraceae: Gnaphalieae)
• Genomics of sable ( <i>Martes zibellina)</i> × pine marten ( <i>Martes martes</i> ) hybridization
• Deciphering phenylalanine-derived salicylic acid biosynthesis in plants
• An integrative taxonomic approach reveals exceptional species diversity of <i>Burmoniscus</i> from China (Crustacea: Isopoda: Oniscidea)
• Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three Spiroplasma (Citri clade) strains associated with Drosophila
• First detection of Sindbis virus in wild birds in Nigeria
• Genomic diversity of clinically relevant bacterial pathogens from an acute care hospital in Suva, Fiji
• Deciphering the Code of Viral-Host Adaptation Through Maximum-Entropy Nucleotide Bias Models
• Genomic diversity and tracing of Paenibacillus larvae in Australia: implications for American foulbrood outbreak surveillance in low-diversity populations
• Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region
• The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree
• Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization
• The Clinical and Molecular Characteristics of Community-Associated <i>Staphylococcus aureus</i> Bacteremia in Persons who Inject Drugs at a New York City Tertiary Care Facility During the Opioid Epidemic
• &lt;i&gt;Unguispora grylli&lt;/i&gt;, a new species of amphibious fungi associated with crickets (&lt;i&gt;Gryllidae&lt;/i&gt;), transforms attachment structures of sporangiola in the host gut.
• Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope ( <i>Hippotragus leucophaeus</i> )
• VCF2Dis: an ultra-fast and efficient tool to calculate pairwise genetic distance and construct population phylogeny from VCF files
• Navigating phylogenetic conflict and evolutionary inference in plants with target-capture data
• There and back again: historical biogeography of neotropical magnolias based on high-throughput sequencing
• Viral Nervous Necrosis due to Betanodavirus: A Case Study in Pot‐Bellied Seahorses (<i>Hippocampus abdominals</i>)
• Diving into Diversity: Haslea berepwari (Bacillariophyceae, Naviculaceae), a new species of marine diatom from New Caledonia
• Biogeographic Implications of Biodiversity Shortfalls in a Mid‐Altitude Desert Ecotone of the Arabian Peninsula
• Pyrus zhaoxuanii (Rosaceae), A new pear species from Danxiashan Mountain, Guangdong, China
• Phylogenomics and biogeography of <i>Guadua</i>: Insights into a neotropical woody bamboo genus
• A new species of Sedum (Crassulaceae) from eastern China based on morphological and molecular evidence
• Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage ‘Asgard’ archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov.
• Characterisation and comparative analysis of mitochondrial genomes of false, yellow, black and blushing morels provide insights on their structure and evolution
• The mitochondrial genome of the deep-sea pyramid urchin <i>Echinocrepis rostrata</i> (Echinoidea: Holasteroida: Pourtalesiidae)
• Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation
• Genomic insights into drought adaptation of the forage shrub <i>Caragana korshinskii</i> (Fabaceae) widely planted in drylands
• A single gene orchestrates androgen variation underlying male mating morphs in ruffs
• Microbial hauberks: composition and function of surface layer proteins in gammaproteobacterial methanotrophs
• Circatidal control of gene expression in the deep-sea hot vent shrimp <i>Rimicaris leurokolos</i>
• Structure and function of the EDEM:PDI ERAD checkpoint complex
• Sustained virologic suppression of multidrug-resistant HIV in an individual treated with anti-CD4 domain 1 antibody and lenacapavir
• Novel adaptive immune systems in pristine Antarctic soils
• Multi-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling
• Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family
• When paleontology meets genomics: complete mitochondrial genomes of two saber-toothed cats’ species (Felidae: Machairodontinae)
• Combining short- and long-read sequencing unveils geographically structured diversity in Borrelia miyamotoi
• Epidemiological data of an influenza A/H5N1 outbreak in elephant seals in Argentina indicates mammal-to-mammal transmission
• The role of family and environment in determining the skin bacterial communities of captive aquatic frogs, <i>Xenopus laevis</i>
• A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets
• Tenkana, a new genus of jumping spiders (Salticidae, Plexippina) from South Asia, with the new Indian species Tenkana jayamangali
• Genomic differentiation and gene flow among <i>Rattus</i> species distributed in China and adjacent regions
• Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia
• Expansion, restructuring and characterization of the <i>Legionellaceae</i> family
• Prominin 1 and Tweety Homology 1 both induce extracellular vesicle formation
• Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape
• Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on <i>Degranvillea dermaptera</i>
• Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria
• Ancient plant-like terpene biosynthesis in corals
• Parallel patterns of genetic diversity and structure in circumboreal species of the <i>Sphagnum capillifolium</i> complex
• Gene transfer among viruses substantially contributes to gene gain of giant viruses
• Predicting multiple conformations via sequence clustering and AlphaFold2
• Mathematics Experience and Format-specific Effects in Numerical Cognition
• Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era
• Genomic coordination of nucleotide skews and gene strand distribution driven by GC‐content in prokaryotes
• Origin and transport of bacterial hopanoids
• Integrative phylogenetic and morphological approach for species delimitation of <i>Heliopora</i> corals, with the description of <i>H. chinensis</i> sp. nov. (Octocorallia: Helioporidae)
• Evolutionary dynamics of enlarged neo-sex chromosomes and novel pseudoautosomal regions in Sylvioidea songbirds
• Neuraminidase reassortment and oseltamivir resistance in clade 2.3.4.4b A(H5N1) viruses circulating among Canadian poultry, 2024
• Isolation and characterization of a clade 2.3.4.4b genotype D1.1 H5N1 virus from dairy cattle in Wisconsin
• Sulfurimonas lacustris sp. nov. and Sulfurimonas limnophila sp. nov. from the chemocline of a meromictic brackish lake
• Evolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology
• Unveiling Global Diversity of Patescibacteriota and Functional Interactions with Host Microbes
• Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
• No Evidence Supports the Presence of SRF-type MADS-Box Genes in Land Plants
• Unravelling the unique essential genes of Streptococcus canis through transposon-directed insertion-site sequencing
• A DNA barcode reference library of terrestrial and freshwater molluscs of Catalonia, northeastern Iberian Peninsula
• Thermus javaensis sp. nov., a novel thermophilic bacterium isolated from litter of a geyser in Cisolok, West Java, Indonesia
• Phylogenomic analysis of vocal fold length evolution reveals links between vocal and auditory systems in terrestrial mammals
• Horizontal Gene Transfers Underpin Ribose Heterotrophy and Central Carbon Metabolism Remodeling in Gloeobacteraceae
• Applications of the Vendi score in genomic epidemiology
• Meta-omic insights into active bacteria mediating N ₂ O mitigation and dissimilatory nitrate reduction to ammonium in an ammonia recovery bioreactor
• Complete mitochondrial genomes of the black corals Alternatipathes mirabilis Opresko &amp;amp; Molodtsova, 2021 and Parantipathes larix (Esper, 1788) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae)
• Ultra-deep sequencing reveals intra-host diversity and co-infection-driven evolution of SARS-CoV-2
• Afzelia corallina (Fabaceae), a new micro-endemic tree from Pemba Island, Zanzibar, Tanzania
• Comparative Genomics Provide Insight Into the Evolution of European <i>Aphanomyces euteiches</i> Strains
• Revisiting Acalypha medicinal interest: ethnobotany, experimental studies, and the implications of taxonomic misuse pitfalls
• Leveraging ancestral sequence reconstruction for protein representation learning
• Four new freshwater crab species of the genus Megapleonum Huang, Shih &amp;amp; Ahyong, 2018 (Crustacea, Decapoda, Potamidae) from Guangdong, China
• A Population Genomics Approach to Understand the Diversity, Migration, and Reproduction of the Rice Pathogen <i>Cercospora janseana</i>
• Bacteriophages mobilize bacterial defense systems via lateral transduction
• Loss of dispersal via ice nucleation activity constrains microbial evolution
• Evolutionary Analysis of Trehalose Breakdown Pathways
• Genomic and Pathogenic Insights into the Geographic Range Expansion of Wheat Blast into Uruguay
• MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes
• Genetic diversity of the freshwater clam Corbicula fluminea from its native range in the mainland Southeast Asia
• Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes
• Host–anellovirus interactions in an island ecosystem: non-human primates and rodents in Madagascar harbour diverse, rich anellovirus populations
• Mycoheterotrophy and plastid genome evolution in the early-diverging epidendroid orchid tribe Nervilieae: independent transitions in <i>Epipogium</i> and <i>Stereosandra</i>
• Novel 20th century rotavirus alphagastroenteritidis strains identified in formalin-fixed and ethanol-preserved museum specimens
• Beet Curly Top Virus Genetic Diversity, Impact on Cannabinoids, Potential Seed Transmission, and Vector Biology in Hemp
• Conspecific Scaffold‐Level Genome Assembly Outperforms Heterospecific Chromosome‐Level Assemblies for Assessing Genetic Indicators in a Threatened Marine Fish
• A case of laboratory-acquired Salmonella Typhi infection due to phage typing in Japan: whole-genome sequencing confirms the source of infection
• Ultraconserved elements, DNA barcoding and morphology unravel the diversity and evolution of the <i>Hypoponera pruinosa</i> group (Hymenoptera: Formicidae) in Indochina and the Indo-Australian region
• Egg Yolk Protein Homologs Identified in Live-Bearing Sharks: Co-Opted in the Lecithotrophy-to-Matrotrophy Shift?
• Living on the Rocks: Genomic Analysis of Limestone Langurs Provides Novel Insights into the Adaptive Evolution in Extreme Karst Environments
• Surrounded: Inoculum Sources of <i>Colletotrichum gloeosporioides</i> Complex Pathogens Around Florida Ericales Crops: Tea, Camellia, and Blueberry
• Exploring the impact of Cenozoic climate change on diversification of the Australian endemic Eurepini crickets (Orthoptera: Gryllidae: Eneopterinae)
• Morphological and genomic data from Belgian naturalised populations reinstate the enigmatic Lathyrus platyphyllos (Fabaceae) as a distinct European species
• Atkinsonella hypoxylon virus capsid structure highlights the diversity of capsid proteins among the Partitiviridae
• Unravelling the cryptic diversity of the low-dispersal land planarian <i>Cephaloflexa bergi</i> to elucidate diversification processes in the Brazilian Atlantic Forest
• When cells rebel: a comparative genomics investigation into marsupial cancer susceptibility
• Full spatio-temporal analyses of migration and colonization in evolution—dense 3D mapping of cancer metastases provides new insights
• Sex-biased gene expression precedes sexual dimorphism in the agonadal annelid <i>Platynereis dumerilii</i>
• Using Gene Trees with Lineage-Specific Duplicates for Phylogenetic Inference Mitigates the Effects of Long-Branch Attraction
• Multiple origins, one function: evolutionary pathways of HSP70 proteins in viruses
• Origin and Evolution of Key Enzymes in the Anammox Pathway Revisited
• On correctness of gene tree tagging under a unified model of gene duplication, loss, and coalescence
• Impatiens tainingensis (Balsaminaceae), a new species from southeastern China
• An archaeal genetic code with all TAG codons as pyrrolysine
• A novel glutathione transferase harboring an <scp>FMN</scp> redox cofactor
• Independent origins of spicules reconcile paleontological and molecular evidence of sponge evolutionary history
• Microendemism can be the rule in the Brazilian Caatinga: evidence from flat lizards of the <i>Tropidurus semitaeniatus</i> group (Squamata: Tropiduridae)
• piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE
• Evolutionary rates provide genomic insights into convergent and lineage-specific evolution in carnivorous plants
• Disordered N‐termini enhance the thermostability of <scp>SGNH</scp> ‐hydrolase family polyesterases
• Evaluating 18S Phylogenetic Placement Accuracy to Uncover Hidden Diversity in Early Branching Animals
• Loss of mitochondrial single stranded DNA-binding protein (mtSSB) gene is associated with mitochondrial genome fragmentation in Psocodea (bark lice, book lice, and parasitic lice)
• Evolutionary dynamics and functional divergence of the UDP-glycosyltransferases gene family revealed by a pangenome-wide analysis in tomato
• Phylogenomic Analysis of Deep-Branching Telonemid
• Ecology and spread of the North American H5N1 epizootic
• Unraveling Epistatic Interactions Between Sites Under Drug-Dependent Selection in the <i>Mycobacterium tuberculosis</i> Genome
• The diversification of the loach genus Schistura McClelland, 1838 (Teleostei, Nemacheilidae) in Sri Lanka
• Collagen fingerprinting and sequence analysis provides a molecular phylogeny of extinct Australian megafauna
• Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding
• Strain-level translocation and enrichment mechanisms of oral bacteria in the lower gastrointestinal tract of stunted children
• Improved Robustness to Gene Tree Incompleteness, Estimation Errors, and Systematic Homology Errors with Weighted TREE-QMC
• Geospatial and phylogenetic clustering of acute and recent HIV infections in Lilongwe, Malawi
• Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases
• Revised evolutionary relationships within Brachycera and the early origin of bicoid in flies
• New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the <i>Pelagibacterales</i>
• Rediscovery and redescription of <i>Cynodonichthys myersi</i> from the mangroves of northern Yucatan Peninsula, Mexico (Cyprinodontiformes, Rivulidae)
• Grass fly evolution unlocked: phylogenomics and classification of worldwide Chloropidae (Diptera)
• The <i>Spirogyra</i> genome: signatures of shared and divergent division and differentiation
• The diversity and abundance of chytrids on the Greenland Ice Sheet – new quantitative data
• Genomic Data Reveals Cryptic Diversity in the Soda Lake Cichlid <scp><i>Oreochromis amphimelas</i></scp>
• The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
• Species boundaries in the subgenus Angelomys (Rodentia: Cricetidae: Abrothrix): A complex case obscured by mitochondrial-species tree discordance
• Camellia guiliangii (Theaceae), a new yellow-flowered Camellia species from limestone mountains of southern Yunnan, China
• Phylogenomic analyses of the Austral podocarps (Podocarpus: Podocarpaceae) support hybrid ancestry of a New Zealand species
• Island hoppers: Integrative taxonomic revision of Hogna wolf spiders (Araneae, Lycosidae) endemic to the Madeira islands with description of a new species
• A Novel Landscape Macrogenetics Approach Reveals Conservation Implications of Australia's 2019–2020 Black Summer Wildfires
• Old goats, new insights: Origins and genetic diversity of feral Cheviot goats
• From Traps to Taxa: Building a Robust <scp>DNA</scp> Barcode Reference Library for the Early Detection of Invasive Cerambycidae
• The hidden sweet tooth of the black soldier fly ( <i>Hermetia illucens</i> )
• Rhododendron jiucaipingensis (Ericaceae), a new species from Guizhou, China
• Genome size evolution in Helianthemum (Cistaceae): Dynamic genomes within a conserved chromosomal framework
• Are interphylum spiralian relationships resolvable?
• Anoxia-adapted cyanobacteria in a marine blue hole
• Conservation profile of the largest Palearctic silverfish and Europe's largest cave-adapted terrestrial insect: Squamatinia algharbica (Zygentoma, Nicoletiidae)
• Mitogenomic phylogeny and timetree of Trematoda: overcoming topological instability
• Dictyolimon gilesii (Plumbaginaceae), a new generic record to China, with special reference to its first plastome
• Occallatibacter bavaricus sp. nov., a new representative of the Acidobacteriota isolated from fen soils, reclassification of Terracidiphilus gabretensis as Occallatibacter gabretensis comb. nov. and emended description of the genus Occallatibacter
• Alloscopus ramanai sp. nov. (Orchesellidae, Heteromurinae), a new Collembola species from central Thailand, with complete mitochondrial genome and phylogenetic placement
• The Goldilocks effect drives plant diversification on middle-aged Hawaiian islands
• Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals
• Slippery slopes: Montane isolation and elevational shifts shape the evolution and diversity of Iberolacerta lizards
• Immunogenicity of a trivalent haemorrhagic fever vaccine candidate against Sudan virus, Marburg virus and Lassa virus in an mpox vaccine
• Gateways to the underworld: molecular phylogenetic analyses identify patterns of groundwater fauna and two new species of hypogean Hyalella Smith, 1874 (Amphipoda, Hyalellidae) from the northern Mojave Desert
• Genomic Assessment of Giraffes in North American Collections Highlights Conservation Challenges
• A ‘Crikey’ new snake: An insular Lycodon Fitzinger, 1826 (Squamata, Colubridae) from the Nicobar Archipelago, India
• A new species of Plagiopholis Boulenger, 1893 (Serpentes, Pseudoxenodontidae) from Guangdong, China
• Rediscovery and molecular phylogenetic placement of the endemic diving beetle Allodessus skottsbergi (Coleoptera: Dytiscidae) in Rano Kau crater of Rapa Nui (Easter Island)
• When islands collide: Divergence predicts outcomes of secondary contact during the fusion of Sulawesi’s paleo-archipelago
• Museum genomics suggests long-term population decline in a putatively extinct bumble bee
• Wnt signaling patterns a central–peripheral body axis in the early-diverging metazoan <i>Trichoplax adhaerens</i>
• Pternopetalum wulingense (Apiaceae), a new species from the Wuling Mountains, China
• A highly contiguous genome assembly for the California vole, <i>Microtus californicus,</i> provides insight into phylogenetic relationships and patterns of synteny among voles
• Acoelomorph flatworm monophyly is a long-branch attraction artefact obscuring a clade of Acoela and Xenoturbellida
• Evolution and comparative genomics of tick-associated <i>Francisella</i> endosymbionts: insights into metabolic pathways and historical biogeographic patterns
• Mriyaviruses: small relatives of giant viruses
• Another case of island gigantism: the extinct Hodgens’ Waterhen (Tribonyx hodgenorum) is a member of Porzana (Aves: Rallidae)
• Petrocosmea pengzhouensis (Gesneriaceae), a new species from Sichuan Province, China
• Cardimyxobolus iriomotensis n. sp. (Cnidaria: Myxosporea: Ortholineidae) parasitic in gill filaments of Rhinogobius species (Gobiiformes: Gobiidae) in Japan
• Population dynamics and evolutionary history of the genus Sakesphorus (Aves: Thamnophilidae) in the Amazonian floodplains
• Estimates of molecular convergence reveal genes with intermediate pleiotropy underlying adaptive variation across teleost fish
• Characterization of Staphylococcus argenteus in Christchurch, New Zealand, and comparison to global strains
• Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development
• Fodinibius alkaliphilus sp. nov., a moderately halophilic and alkaliphilic bacterium isolated from an inland saltern in central Portugal and reclassification of Aliifodinibius salipaludis as Fodinibius salipaludis sp. nov.
• Inferring Species Trees
• Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene <i>LAR</i>
• Phyling: phylogenetic inference from annotated genomes
• Mind the gap: DNA barcoding on Pachygrapsus crabs
• The reconstructed evolutionary history of the <i>Engelhardia spicata</i> complex highlights the impact of a three‐tiered landform in the Indo‐Burma ecoregion
• Characterization of the mitochondrial genomes for Ophiostoma ips and related taxa from various geographic origins and related species: large intron-rich genomes and complex intron arrangements
• Spatio-temporal dynamics of Hendra virus in Pteropus bats in Australia reveals high evolutionary diversity linked with spillover
• CRESSENT: a Bioinformatic Toolkit to Explore and Improve ssDNA Virus Annotation
• Genomic epidemiology of SARS-CoV-2 in Norfolk, UK, March 2020–December 2022
• Faster adaptation but slower divergence of X chromosomes under paternal genome elimination
• Systematics and historical biogeography of <i>Crunomys</i> and <i>Maxomys</i> (Muridae: Murinae), with the description of a new species from Sulawesi and new genus-level classification
• The evolution of function in the DNA binding domain of the CRP/FNR family
• Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid <i>Prunus</i> (Rosaceae)
• High-resolution genome assembly and population genetic study of the endangered maple <i>Acer pentaphyllum</i> (Sapindaceae): implications for conservation strategies
• Detection of clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus in a sheep in Great Britain, 2025
• Revision of the cockroach subfamily Blattinae based on morphological and molecular analyses
• Fine-tuned terpene synthase gene expression, functional promiscuity, and subcellular localization: implications for the evolution of complex floral volatile bouquet in <i>Caladenia</i> orchids
• Tracing the Origin of the 2022 Dengue Virus Epidemic in Karachi, Pakistan, Through Genome Analyses
• Disruption of HaVipR1 confers Vip3Aa resistance in the moth crop pest Helicoverpa armigera
• Telomere-to-telomere genome of common bean (<i>Phaseolus vulgaris</i> L., YP4)
• Genomic and <i>Cis</i> ‐Regulatory Basis of a Plastic C ₃ ‐C ₄ Photosynthesis in <i>Eleocharis Baldwinii</i>
• Gag proteins encoded by endogenous retroviruses are required for zebrafish development
• Metagenomic Sequencing of Tomato Plants with Wilt Symptoms Allows for Strain-Level Pathogen Identification and Genome-Based Characterization
• Phylogenetic evidence reveal a close relationship between Amphichorda and Ovicillium in Bionectriaceae (Hypocreales)
• Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis
• High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens)
• Population genomics of Vitis pseudoreticulata reveals the genetic basis of fungal resistance in grapevine
• Endemic transmission of a Mycobacterium tuberculosis L2.2.M3 sublineage of the L2 lineage within Colon, Panama: A prospective study
• Studies of Vietnamese Pteridophyte Flora 3
• Coalescent-delimitation framework disentangles species boundaries within the Neotropical mouse-opossums subgenus <i>Marmosops</i>
• The Unexplored Biodiversity of ‘Glacier Fleas’ (Hexapoda: Collembola): Taxonomy, Distribution and Ecology in the European Alps and Apennines
• Genomic and transcriptomic analyses of <i>Heteropoda venatoria</i> reveal the expansion of P450 family for starvation resistance in spiders
• The complete mitochondrial genome of the ‘Extinct in the Wild’ Spix’s Macaw (Cyanopsitta spixii)
• Tissue-like multicellular development triggered by mechanical compression in archaea
• A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat
• Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France
• Catalogue of fungi in China 6: <i>Rhytismataceae</i> on twigs of <i>Rhododendron</i>
• Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)
• Phycocyanobilin Binding and Specific Amino Acid Residues Near The Chromophore Contribute To Orange Light Perception By The Dualchrome Phytochrome Region
• Role of public DNA-Seq data in mitogenomics research: A case study on the flying fish family (Beloniformes: Exocoetidae)
• Increased immunogen valency improves the maturation of vaccine-elicited HIV-1 VRC01-class antibodies
• Virome Scanning of Pear Germplasm Collections Identifies a New Velarivirus and Extends the Geographical Spread of Three Other Pear Viruses
• Genomic insights into the beneficial potential of Bifidobacterium and Enterococcus strains isolated from Cameroonian infants
• IMA GENOME - F20 A draft genome assembly of Agroathelia rolfsii, Ceratobasidium papillatum, Pyrenopeziza brassicae, Neopestalotiopsis macadamiae, Sphaerellopsis filum and genomic resources for Colletotrichum spaethianum and Colletotrichum fructicola
• Assessing the genetic composition of invasive knotweeds (<i>Reynoutria</i>, Polygonaceae) using data from the first intron and second exon of the nuclear <i>LEAFY</i> gene
• Draft genome of the endemic alpine ground beetle <i>Carabus</i> (<i>Platycarabus</i>) <i>depressus</i> (Coleoptera: Carabidae) from long-read sequencing of a frozen archived specimen
• Mitochondrial genome and transcription of Shiraia-like species reveal evolutionary aspects in protein-coding genes
• Evolution and spread of Xanthomonas citri subsp. citri in the São Paulo, Brazil, citrus belt inferred from 758 novel genomes
• Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of Crataegus shandongensis (Rosaceae, Maleae)
• Functional trait mismatch between native and introduced bee pollinators servicing a global fruit crop
• Will the real invasive snail please stand up? A phylogenetic reconsideration of <i>Paralaoma servilis</i> (Shuttleworth, 1852) (Gastropoda: Stylommatophora: Punctidae)
• Evaluating the stability of nursery-established arbuscular mycorrhizal fungal associations in apple rootstocks
• Discovery of three rare acremonium-like fungi in the rhizosphere of Gaultheria leucocarpa var. yunnanensis resolves the sister relationship between <i>Paraneoaraneomyces</i> and <i>Subuliphorum</i> (Clavicipitaceae, Hypocreales).
• Insect Antimicrobial Peptides as Guardians of Immunity and Beyond: A Review
• Convergent origin and accelerated evolution of vesicle-associated RhoGAP proteins in two unrelated parasitoid wasps
• High-throughput algorithm predicts F-Type ATP synthase rotor ring stoichiometries of 8 to 27 protomers
• Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus
• Spotty distributions: Spotted Gar (Lepisosteus oculatus) and Spotted Sucker (Minytrema melanops) range expansion in eastern Lake Erie
• Phylogenomic and demographic history of the Cape cliff lizard ( <i>Hemicordylus capensis</i> )
• Identification, Distribution, and Pathogenicity of <i>Lasiodiplodia</i> Species Causing Avocado Stem-End Rot in Peru
• Feeding Strategy Shapes the Evolution of the Hyaluronidase Gene Family in Medicinal Leeches
• GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics
• Evolution of a bipolar sexual compatibility system in <i>Marasmius</i>
• Genomic survey of the ex situ Palm Cockatoo (Probosciger aterrimus) population identifies an undiscovered species-level lineage endemic to Yapen Island
• Derlin-like proteins are essential for the function of <i>Euglena gracilis</i> chloroplasts
• Increased abundance of <i>Limosilactobacillus reuteri</i> in the gut of selectively bred high-tameness mice and its association with behavioural changes
• Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs
• <i>Pseudocercospora oenotherae</i> Causing Leaf Spot on Ornamental <i>Lantana strigocamara</i> : Characterization and Host Resistance
• Genetic diversity of pangolin coronaviruses reveals a key immuno-evasive substitution at spike residue 519
• Integrative taxonomic revision of Uropsilus (Uropsilinae, Talpidae) combining genomic, morphological and geographic evidence
• Large-scale mitogenome analysis reveals complex maternal genetic connections between Sino-Tibetan- and Altaic-speaking populations
• Evolutionary Rate Variation at Predicted PTM Sites Reveals Localized Host-Associated Patterns in Influenza A Virus
• Tracing the Origin of <i>Xylella fastidiosa</i> subspecies <i>pauca</i> ST53 Strains in France
• Evolution of developmental bias explains divergent patterns of phenotypic evolution in two nematode clades
• Diversity and Structure of <i>Diaporthe humulicola</i> Populations from Eastern North America
• Exposure of termites and associated prokaryotes to soil mercury in a tropical rainforest (French Guiana)
• Nicotinamide Adenine Dinucleotide (NAD ⁺ ) Induces Defense Responses Against Powdery Mildew and Regulates <i>LecRLK</i> Gene Expression in Squash
• Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection
• Divergent Evolutionary Routes of Hypoxia Tolerance in Mangroves
• Target capture efficiently resolves the long‐standing taxonomic dead end of <i>Diachrysia</i> moths
• Global genomic diversity of temperate P2-like viruses
• On the consistency of duplication, loss, and deep coalescence gene tree parsimony costs under the multispecies coalescent
• Integrative taxonomy of the <i>Praomys tullbergi</i> complex (Rodentia, Muridae): a new species from West Africa
• Carbon monoxide oxidation expands the known metabolic capacity in anaerobic methanotrophic consortia
• Unraveling the Diversity and Pathogenicity of Botryosphaeriales Species Causing Stem Blight and Dieback of Blueberries in Sinaloa, Mexico
• Rapid mid-Cretaceous diversification of squid and cuttlefish preceded radiation into coastal niches
• DNA barcoding of non-indigenous fish species in the Volga-Kama basin: assessment of current taxonomic assignment and differentiation in the Ponto-Caspian Basin
• The Late Quaternary climate impact on the genome of the woodland strawberry (Fragaria vesca), a perennial herb
• Defensomes, counter-defensomes, and the remodeling of microbial communities
• Two decades (2005 to 2025) of avian influenza research trends, knowledge gaps and distribution of emerging H5N1 2.3.4.4b clade in South Asia
• piqtree: a python package for seamless phylogenetic inference with IQ-TREE
• A new species of Dondersiidae (Mollusca, Solenogastres) associated with a hydroid, with insights into the trophic ecology of Solenogastres
• A comprehensive analysis of the SARS-CoV-2 omicron variant in Tocantins State, Brazil, and tracing the spread of the XBB.1.18.1 lineage
• Phylogenomic insights into the first multicellular streptophyte
• Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae
• Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield
• Identification and characterization of <i>Cladosporium</i> species associated with tea plants ( <i>Camellia sinensis</i> ) in China
• Comparative genomics of endemic <i>Staphylococcus aureus</i> ST1 in New Zealand
• Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids
• Mitochondrial DNA 16S region and voucher specimen collection of Japanese aquatic Coleoptera and Hemiptera for environmental DNA metabarcoding analyses
• Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles
• The role of toxin/antidote genes in the maintenance and evolution of accessory chromosomes in <i>Fusarium</i>
• Evolutionary Diversification and Functions of the Candidate Male Killing Gene <i>wmk</i>
• Phylogenomic Analyses Reveal that <i>Panguiarchaeum</i> Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia
• The tiniest genomes shrink much further: extreme reductive evolution in planthopper symbionts
• Molecular phylogeny and body size-related convergent evolution of nesting behaviour in small dung beetles (Coleoptera: Scarabaeidae: Aphodiinae)
• Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush
• But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating
• Molecular identification of whole squids and calamari at fairs and markets in regions of Latin America
• High‐quality genome of allotetraploid <i>Avena barbata</i> provides insights into the origin and evolution of B subgenome in <i>Avena</i>
• Large-scale Genome Analyses Provide Insights into Hymenoptera Evolution
• Phylogenomic insights into the relationship and the evolutionary history of planthoppers (Insecta: Hemiptera: Fulgoromorpha)
• Explaining extreme differences in species richness among co-occurring palm clades in Madagascar
• Going deep: phylogenomic analyses incorporating museomic data reveal divergence and character evolution in Decapodiformes (Mollusca: Cephalopoda)
• Population structure and gene flux of Listeria monocytogenes ST121 reveal prophages as a candidate driver of adaptation and persistence in food production environments
• Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming
• New Iflavirus identified in Chiroxiphia pareola birds from an ecotone area in northeast Brazil
• Comparative and subtractive genomics reveals novel therapeutic targets in cystic fibrosis-associated multidrug-resistant Pandoraea sputorum
• A new species of fossorial snake of the genus Trachischium Günther, 1858, from the Indo–Burma biodiversity hotspot
• Repeated emergence of giant microRNA hairpins across invertebrates
• The origin and diversification of Amaryllidaceae: A phylogenetic and biogeographic analysis
• Saliva Protein Genes in Humans were Shaped During Primate Evolution
• Diagnosing Systematic Errors and Incomplete Lineage Sorting in the Deep Phylogeny of Collembola
• Out‐of‐Africa: Origin of the Disjunct Distribution of Paleotropical Eneopterinae Crickets (Gryllidae, Xenogryllini)
• Experiences with Model Context Protocol Servers for Science and High Performance Computing
• Phylotranscriptomic analyses reveal the reticulate evolution in Dennstaedtiaceae
• A shallow‐scale phylogenomics approach reveals repeated patterns of diversification among sympatric lineages of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)
• Evidence that Zymocin-Like Killer Plasmids Were Present in the Common Ancestor of Terrestrial Fungi
• Discordance Down Under: Combining Phylogenomics and Fungal Symbioses to Detangle Difficult Nodes in a Diverse Tribe of Australian Terrestrial Orchids
• Phylogenomics and the evolutionary history of the Oxyurida (pinworms)
• Characteristics of vhvp-2 gene distribution and diversity within the Vibrio causing translucent post-larvae disease (TPD)
• Concordance and Discordance in the Phylogenomics of the Wrasses and Parrotfishes (Teleostei: Labridae)
• Inference of germinal center evolutionary dynamics via simulation-based deep learning
• Evolutionary analysis of ascorbate-glutathione cycle genes across green plants with lineage-specific profiling in grapevine ( <i>Vitis vinifera</i> L.)
• Dynamics of natural selection preceding human viral epidemics and pandemics
• <i>Botrytis michiganensis</i> : A New <i>Botrytis</i> Species Causing Blossom Blight on Highbush Blueberries
• A deep-time landscape of plant <i>cis</i> -regulatory sequence evolution
• Phylogenetic review of the millipede genus Cherokia Chamberlin, 1949 (Polydesmida, Xystodesmidae)
• DNA barcoding reference dataset revealed overlooked diversity and clarified biogeography of fishes in the largest European river system – Volga River
• Phylogenetic position and revised classification of <i>Trichonectria</i> (Hypocreales) and related genera
• Genomic analysis of <i>Ostreococcus tauri</i> -infecting viruses reveals a hypervariable region associated with host–virus interactions
• Primula daguanensis (Primulaceae), a new species from Yunnan, China
• <tt>torchtree</tt> : Flexible Phylogenetic Model Development and Inference Using PyTorch
• Elevated temperature simulating heatwaves restructures active nitrifying communities and associated viruses in tidal flats and agricultural soils
• Morphology, genetic characterization and mitochondrial genome of Gorgorhynchus fistularius sp. nov. (Acanthocephala, Isthmosacanthidae) from the red cornetfish Fistularia petimba (Lacépède, 1803) (Gasterosteiformes, Fistulariidae), with phylomitogenomics of the family Isthmosacanthidae
• A dual-factor complex governs archaeal ribosome hibernation by sensing energy status
• Redescription and systematics of Oligodon ornatus Van Denburgh, 1909, and two enigmatic related species (Squamata, Colubridae)
• Multiple protein structure alignment at scale with FoldMason
• Mitochondrial genome and phylogenetic placement of the enigmatic mole beetle, <i>Hypocephalus armatus</i> Desmarest, 1832 (Coleoptera: Chrysomeloidea)
• FastSpeciesTree: Fast and Scalable Species tree Inference
• Genome-wide, evolutionary, and stress-responsive landscape of the Pectin methylesterase gene family in cucumber and muskmelon
• A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit
• A large phylogenetic tree for euphyllophytes
• Evolution of Duplicated Hox Gene Clusters in Land Snails and Slugs
• Phylogenomics, trophic ecology, and systematics of the <i>Morchellaceae</i>

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